Magnesium in PDB 6om4: The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca
Protein crystallography data
The structure of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca, PDB code: 6om4
was solved by
S.-H.Dong,
S.K.Nair,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
65.98 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.094,
76.059,
131.902,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.5 /
19.9
|
Other elements in 6om4:
The structure of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca
(pdb code 6om4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca, PDB code: 6om4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6om4
Go back to
Magnesium Binding Sites List in 6om4
Magnesium binding site 1 out
of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:17.2
occ:1.00
|
O
|
A:HOH518
|
2.1
|
17.7
|
1.0
|
O
|
A:HOH516
|
2.1
|
22.7
|
1.0
|
O
|
A:HOH591
|
2.1
|
17.9
|
1.0
|
O6
|
A:POP403
|
2.1
|
15.6
|
1.0
|
OD2
|
A:ASP148
|
2.1
|
18.6
|
1.0
|
O
|
A:HOH585
|
2.2
|
18.4
|
1.0
|
CG
|
A:ASP148
|
3.1
|
18.8
|
1.0
|
P2
|
A:POP403
|
3.3
|
16.6
|
1.0
|
OD1
|
A:ASP148
|
3.5
|
17.4
|
1.0
|
O5
|
A:POP403
|
3.6
|
16.5
|
1.0
|
NZ
|
A:LYS170
|
4.0
|
16.5
|
1.0
|
OE1
|
A:GLU151
|
4.1
|
27.8
|
1.0
|
O
|
A:GLN149
|
4.1
|
20.1
|
1.0
|
CD
|
A:GLU151
|
4.1
|
27.4
|
1.0
|
O3
|
A:POP403
|
4.2
|
18.8
|
1.0
|
O
|
A:POP403
|
4.2
|
17.2
|
1.0
|
OE2
|
A:GLU151
|
4.2
|
29.4
|
1.0
|
OD1
|
A:ASN154
|
4.3
|
19.1
|
1.0
|
ND2
|
A:ASN154
|
4.3
|
12.1
|
1.0
|
O4
|
A:POP403
|
4.4
|
18.3
|
1.0
|
CB
|
A:ASP148
|
4.4
|
18.7
|
1.0
|
CE
|
A:LYS170
|
4.5
|
16.4
|
1.0
|
CG
|
A:ASN154
|
4.8
|
15.4
|
1.0
|
CG
|
A:GLU151
|
4.8
|
23.1
|
1.0
|
P1
|
A:POP403
|
4.9
|
17.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6om4
Go back to
Magnesium Binding Sites List in 6om4
Magnesium binding site 2 out
of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:17.3
occ:1.00
|
O2
|
A:POP403
|
2.0
|
18.3
|
1.0
|
O1A
|
C:ND7101
|
2.0
|
18.8
|
1.0
|
O5
|
A:POP403
|
2.0
|
16.5
|
1.0
|
O
|
A:HOH623
|
2.1
|
18.8
|
1.0
|
O
|
A:HOH568
|
2.2
|
15.9
|
1.0
|
O
|
A:HOH532
|
2.3
|
15.3
|
1.0
|
P2
|
A:POP403
|
3.2
|
16.6
|
1.0
|
P1
|
A:POP403
|
3.2
|
17.9
|
1.0
|
O
|
A:POP403
|
3.4
|
17.2
|
1.0
|
PA
|
C:ND7101
|
3.5
|
21.3
|
1.0
|
O4
|
A:POP403
|
3.8
|
18.3
|
1.0
|
O3
|
A:POP403
|
3.9
|
18.8
|
1.0
|
O
|
A:HOH627
|
4.1
|
24.6
|
1.0
|
OD2
|
A:ASP214
|
4.1
|
21.4
|
1.0
|
O
|
A:HOH521
|
4.1
|
19.4
|
1.0
|
O
|
A:HOH530
|
4.1
|
26.4
|
1.0
|
O
|
A:HOH585
|
4.2
|
18.4
|
1.0
|
N3A
|
C:ND7101
|
4.3
|
19.7
|
1.0
|
O5'
|
C:ND7101
|
4.3
|
19.5
|
1.0
|
OD1
|
A:ASP214
|
4.3
|
20.7
|
1.0
|
C5'
|
C:ND7101
|
4.3
|
18.9
|
1.0
|
O1
|
A:POP403
|
4.4
|
17.9
|
1.0
|
O6
|
A:POP403
|
4.4
|
15.6
|
1.0
|
O2A
|
C:ND7101
|
4.5
|
18.9
|
1.0
|
CG
|
A:ASP214
|
4.6
|
21.2
|
1.0
|
C3'
|
C:ND7101
|
4.8
|
18.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6om4
Go back to
Magnesium Binding Sites List in 6om4
Magnesium binding site 3 out
of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:30.2
occ:1.00
|
O3
|
B:POP404
|
1.9
|
26.4
|
1.0
|
O
|
B:HOH587
|
2.0
|
24.5
|
1.0
|
OD2
|
B:ASP148
|
2.1
|
27.9
|
1.0
|
O
|
B:HOH504
|
2.1
|
30.6
|
1.0
|
O
|
B:HOH589
|
2.2
|
27.2
|
1.0
|
CG
|
B:ASP148
|
3.2
|
29.2
|
1.0
|
P1
|
B:POP404
|
3.3
|
26.1
|
1.0
|
O1
|
B:POP404
|
3.6
|
22.8
|
1.0
|
OE2
|
B:GLU151
|
3.7
|
50.0
|
1.0
|
CD
|
B:GLU151
|
3.7
|
37.8
|
1.0
|
OD1
|
B:ASP148
|
3.7
|
29.0
|
1.0
|
OE1
|
B:GLU151
|
3.9
|
40.3
|
1.0
|
NZ
|
B:LYS170
|
4.0
|
22.4
|
1.0
|
O
|
B:GLN149
|
4.1
|
19.0
|
1.0
|
O
|
B:POP404
|
4.1
|
24.8
|
1.0
|
OD1
|
B:ASN154
|
4.2
|
20.8
|
1.0
|
O4
|
B:POP404
|
4.2
|
23.1
|
1.0
|
O2
|
B:POP404
|
4.2
|
25.0
|
1.0
|
CE
|
B:LYS170
|
4.3
|
18.5
|
1.0
|
ND2
|
B:ASN154
|
4.3
|
13.2
|
1.0
|
CG
|
B:GLU151
|
4.3
|
29.5
|
1.0
|
CB
|
B:ASP148
|
4.5
|
23.9
|
1.0
|
CG
|
B:ASN154
|
4.7
|
17.6
|
1.0
|
P2
|
B:POP404
|
4.9
|
24.6
|
1.0
|
CB
|
B:GLU151
|
4.9
|
23.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6om4
Go back to
Magnesium Binding Sites List in 6om4
Magnesium binding site 4 out
of 4 in the The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of The Structure of Microcin C7 Biosynthetic Enzyme Mccb in Complex with N-Formylated Mcca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg403
b:21.0
occ:1.00
|
O6
|
B:POP404
|
2.0
|
24.1
|
1.0
|
O1
|
B:POP404
|
2.0
|
22.8
|
1.0
|
O2A
|
D:ND7101
|
2.1
|
20.7
|
1.0
|
O
|
B:HOH526
|
2.1
|
20.3
|
1.0
|
O
|
B:HOH576
|
2.1
|
23.0
|
1.0
|
O
|
B:HOH545
|
2.1
|
17.0
|
1.0
|
P1
|
B:POP404
|
3.2
|
26.1
|
1.0
|
P2
|
B:POP404
|
3.3
|
24.6
|
1.0
|
PA
|
D:ND7101
|
3.5
|
19.8
|
1.0
|
O
|
B:POP404
|
3.5
|
24.8
|
1.0
|
OD2
|
B:ASP214
|
4.0
|
17.8
|
1.0
|
O2
|
B:POP404
|
4.0
|
25.0
|
1.0
|
O
|
B:HOH517
|
4.0
|
24.2
|
1.0
|
O4
|
B:POP404
|
4.0
|
23.1
|
1.0
|
O
|
B:HOH589
|
4.2
|
27.2
|
1.0
|
OD1
|
B:ASP214
|
4.2
|
17.2
|
1.0
|
N3A
|
D:ND7101
|
4.2
|
18.0
|
1.0
|
C5'
|
D:ND7101
|
4.4
|
19.5
|
1.0
|
O5'
|
D:ND7101
|
4.4
|
17.7
|
1.0
|
O
|
D:HOH208
|
4.4
|
28.5
|
1.0
|
O3
|
B:POP404
|
4.5
|
26.4
|
1.0
|
O5
|
B:POP404
|
4.5
|
25.6
|
1.0
|
O1A
|
D:ND7101
|
4.5
|
20.5
|
1.0
|
CG
|
B:ASP214
|
4.5
|
17.0
|
1.0
|
O
|
B:HOH704
|
4.7
|
29.5
|
1.0
|
C3'
|
D:ND7101
|
4.8
|
19.1
|
1.0
|
|
Reference:
S.H.Dong,
A.Kulikovsky,
I.Zukher,
P.Estrada,
S.Dubiley,
K.Severinov,
S.K.Nair.
Biosynthesis of the Ripp Trojan Horse Nucleotide Antibiotic Microcin C Is Directed By Then-Formyl of the Peptide Precursor. Chem Sci V. 10 2391 2019.
ISSN: ISSN 2041-6520
PubMed: 30881667
DOI: 10.1039/C8SC03173H
Page generated: Tue Oct 1 13:26:13 2024
|